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revision 1405, Mon Aug 21 14:43:00 2006 UTC revision 1635, Tue Oct 17 21:21:44 2006 UTC
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1    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
4            * tests/matprod.R: add tests for the bug fixed.
5    
6    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
9            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
10    
11    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
12    
13            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
14    
15    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * DESCRIPTION (Version): 0.9975-3
18    
19            * R/diagMatrix.R (bdiag): new function constructing block diagonal
20            (sparse) matrices.
21            * man/bdiag.Rd: docu + examples
22    
23            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
24    
25            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
26            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
27    
28            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
29            that result is sparse or diagonal (and not dense).
30    
31            * man/Subassign-methods.Rd: fix examples
32    
33            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
34            should always return a sparse (and not sometimes a diagonal) matrix.
35    
36    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
39    
40    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
41    
42            * DESCRIPTION (Version): 0.9975-2
43    
44            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
45    
46    2006-10-02  Douglas Bates  <bates@R-project.org>
47    
48            * tests/dg_Matrix.R: Simplify test taking into account new code.
49    
50    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
53    
54            * R/lsTMatrix.R: new files w/ missing methods
55            * R/nsTMatrix.R:  "  'for completeness'
56    
57            * tests/Class+Meth.R: a bit less 'not.ok.classes'
58    
59            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
60    
61    
62    2006-09-28  Douglas Bates  <bates@R-project.org>
63    
64            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
65            included.
66    
67            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
68            Export C-callable functions used in Zt_create in lme4.
69    
70    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * DESCRIPTION (Version): 0.9975-1
73    
74            * tests/simple.R: less checks fail; using NA, found that our
75                    kronecker() is not base-compatible with NA's.
76    
77            * R/dMatrix.R: "Compare" method now implemented for all cases
78    
79            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
80    
81            * man/dtpMatrix-class.Rd: mention length of 'x' slot
82    
83            * src/dtpMatrix.c (dtpMatrix_validate): fix check
84            * src/dspMatrix.c (dspMatrix_validate): ditto
85    
86            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
87              including coercion to [nl]tTMatrix.
88    
89            * R/diagMatrix.R (show): print a header line as for other classes.
90    
91    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * src/Makefile.win (SUBDIRS): fix typo
94    
95    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
98    
99    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
100    
101            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
102            symmetric and y missing in R code using %*% (cholmod_aat doesn't
103            accept a symmetric matrix).
104            * tests/group-methods.R: Uncomment test of crossprod applied to
105            lsCMatrix objects.
106    
107    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/AllClass.R (symmetricMatrix): add validity method (available
110            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
111    
112            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
113    
114            * tests/indexing.Rout.save:
115            * tests/indexing.R: additions, mainly for 'lsparse'
116    
117            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
118            case.
119    
120            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
121    
122    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
125                    as 'N' (1-letter - Ok?)
126    
127            * tests/group-methods.R: add test for logical + NAs
128    
129            * R/dMatrix.R ("Compare"): fix to work with NA's
130    
131            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
132    
133            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
134                    which is implemented.
135    
136    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * src/chm_common.c: coerce logical <-> double instead of
139            typecasting;  needed for "l" matrix handling in cholmod.
140    
141            * tests/other-pkgs.R (graph): small extension in "graph" checks.
142    
143            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
144            (Tsp2grNEL): other fixes needed
145    
146    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
149                    Matrices, since "lMatrix", also "lsparseM" can have NA
150            * R/ndenseMatrix.R, etc: new source files
151            * man/nsparseMatrix-classes.Rd, etc: new help files
152            * tests/: adaptions
153            * src/chm_common.c (chm_dense_to_SEXP): and others:
154                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
155            * src/Csparse.c, etc: ditto
156    
157    2006-09-11  Douglas Bates  <bates@R-project.org>
158    
159            * src/Mutils.[ch],init.c inst/include/*.h: Move the
160            alloc_d**Matrix functions to the lme4 package.
161    
162    2006-09-09  Douglas Bates  <bates@R-project.org>
163    
164            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
165            fixed
166    
167    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/lMatrix.R: new
170    
171            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
172    
173            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
174            * man/tcrossprod.Rd: ditto
175    
176    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
177    
178            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
179            for exported functions
180            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
181            Remove partitioning algorithms for sparse matrix reordering.  The
182            copyright on the Metis code was problematic and the methods were
183            rarely used.
184            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
185            operations are now done entirely in CHOLMOD code.
186    
187    2006-09-06  Douglas Bates  <bates@R-project.org>
188    
189            * src/Mutils.h: Remove functions that are no longer used.
190    
191    2006-09-04  Douglas Bates  <bates@R-project.org>
192    
193            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
194            * src/DEPS.mkf: update
195    
196    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * created branches/Matrix-for-R-2.3.x;  on trunk: do
199            * DESCRIPTION (Version): 0.9975-0
200            (Depends): R (>= 2.4.0)
201    
202    2006-09-01  Douglas Bates  <bates@R-project.org>
203    
204            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
205    
206    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
209            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
210    
211            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
212    
213    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
216            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
217            * R/dsparseMatrix.R: ditto
218            * R/Csparse.R: ditto
219    
220    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * R/dMatrix.R (Compare): improve availability of "<", etc
223            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
224    
225    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
228            of a 0-index which was used as 1-index (..hmm)
229    
230            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
231    
232            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
233            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
234            (.is.diagonal): ditto
235    
236            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
237    
238            * R/Matrix.R (Matrix): also work for NA data
239    
240    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
243            in all cases.
244    
245    2006-08-27  Douglas Bates  <bates@R-project.org>
246    
247            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
248            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
249    
250    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
253            subclasses of "ddenseMatrix"
254            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
255            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
256            instead of half dozen specialized ones.
257    
258    2006-08-25  Douglas Bates  <bates@R-project.org>
259    
260            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
261            <tillard@cirad.fr> - ordering standard errors to match effects.
262    
263    2006-08-24  Douglas Bates  <bates@R-project.org>
264    
265            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
266            on R_ldl.
267            * R/lCholCMatrix.R,
268            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
269            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
270            * many files in ./R and ./src: Use more general version of
271            dup_mMatrix_as_dgeMatrix to simplify method definitions.
272            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
273            dtpMatrix, dspMatrix and dppMatrix conversions.
274    
275    
276    2006-08-23  Douglas Bates  <bates@R-project.org>
277    
278            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
279            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
280            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
281            dgeMatrix_crossprod (may need to do this in other places).
282            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
283            generic and method for dsCMatrix.  Use CHOLMOD for chol().
284    
285    2006-08-22  Douglas Bates  <bates@R-project.org>
286    
287            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
288            types of classed Matrices, matrices or numeric or logical vectors.
289            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
290            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
291            to Mutils.h (as an inline) and change name to Matrix_check_class;
292            fixes in as_cholmod_factor and chm_factor_to_SEXP.
293            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
294            dsCMatrix_matrix_solve.  Comment out vestigial functions.
295            * src/Csparse.c: use diag_P and uplo_P macros.
296    
297  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
298    
299          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
300          valgrind.          valgrind.
301            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
302            inverses.
303            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
304            -Wall warnings.
305            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
306            Use dup_mMatrix_as_dgeMatrix.
307    
308  2006-08-20  Douglas Bates  <bates@R-project.org>  2006-08-20  Douglas Bates  <bates@R-project.org>
309    

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